# Fatal Error: atom X in multiple T-coupling groups **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [September 27, 2022, 11:56am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887 "2022-09-27T11:56:20Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![tan2](https://avatars.discourse-cdn.com/v4/letter/t/958977/32.png) [@tan2](https://gromacs.bioexcel.eu/u/tan2)\ **Post date:** [September 27, 2022, 11:56am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/1 "2022-09-27T11:56:20Z")
GROMACS version: 2020.6 GROMACS modification: Yes/No I am getting this following error although I have added both the Protein/ Non protein groups Fatal error: Atom 4812 in multiple T-Coupling groups (1 and 2) Kindly help me ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 29, 2022, 3:08am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/2 "2022-09-29T03:08:34Z")
What is atom 4812? What have you specified in your `tc-grps` setting? Somehow you have created two groups that overlap such that they both include this atom, which is not allowed. ---
**Author:** ![tan2](https://avatars.discourse-cdn.com/v4/letter/t/958977/32.png) [@tan2](https://gromacs.bioexcel.eu/u/tan2)\ **Post date:** [September 29, 2022, 4:50am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/3 "2022-09-29T04:50:26Z")
I created an index file wherein I merged my protein and ligand molecules. This is what I have specified in my tc groups ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein\_UNL non-Protein ; two coupling groups - more accurate tau\_t = 0.1 0.1 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 29, 2022, 11:04am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/4 "2022-09-29T11:04:53Z")
A ligand molecule falls within the default Non-Protein group. You need to create a different group that does not include the ligand if you are merging it with the Protein group. ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [January 16, 2023, 7:12am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/5 "2023-01-16T07:12:33Z")
> [@jalemkul](#): > > 4812 Hi I am also facing the same problem. I want to see the interaction between ligand and the specific residue of Protein. For that, I have created an additional group in index file named [R\_001] which has the first 3563 atoms. additional group in index.ndx ```auto [R_001] 1 2 3 4 5 6 7 8 9 10 ....... 3563 ``` in mdp file, I have defined two energy groups in mdp file ```auto tc-grps = Protein_LIG Water_and_ions energygrps = LIG R_001 ``` I am facing the error “Atom 3453” in multiple Mon. groups (2 and 2). I have checked both groups (LIG and R\_001) thoroughly and found that 3453 is only in **R\_001**. **LIG** doesn’t have Atom number 3453. Why am I getting this error? Thanks ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 16, 2023, 11:41am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/6 "2023-01-16T11:41:16Z")
A single protein residue should never span thousands of atoms. Your group is constructed incorrectly. ---
**Author:** ![shivam1](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Post date:** [January 17, 2023, 12:09am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/7 "2023-01-17T00:09:48Z")
Hi @jalemkul Thanks for your kind reply. However I fixed the problem. I think there was some problem with the .ndx file writing system. When I deleted those atoms and re-write them manually it fixed the error. (not sure though if it occurs again) ---
**Author:** ![mariasharif](https://avatars.discourse-cdn.com/v4/letter/m/a4c791/32.png) [@mariasharif](https://gromacs.bioexcel.eu/u/mariasharif)\ **Post date:** [June 5, 2024, 4:50am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-x-in-multiple-t-coupling-groups/4887/8 "2024-06-05T04:50:21Z")
I faced similar problem I solved by making the index file again gmx make\_ndx -f em.gro -o index.ndx then I select both protein and ligand 1|13 and created a new group name 22 Protein\_UNK hit enter reselect the newly created group i.e. 22 q error was resolved